Major Quantitative Locus Research Articles

Detecting QTLs controlling chlorophyll fluorescence parameters in Iranian wheat recombinant inbred lines

Measurement of chlorophyll fluorescence is one of the methods to detect a disorder in the photosynthetic system, which reflects the photochemical state of the plant. Identification of the genetic structure of chlorophyll fluorescence parameters can provide useful solutions for breeding varieties with higher potential. The present study was conducted with the aim of identifying quantitative loci (QTL) related to chlorophyll fluorescence parameters in an Iranian RILs wheat population. One hundred and twenty F8 RILs of wheat derived from crossing Kohdasht (KHD) and Gonbad (GND) cultivars in the form of an alpha lattice design were studied in 2019 and 2020. The analysis of QTLs was performed in the software R using the package QTL.gCIMapping.GUI v2.0. The genetic map was constructed with 423 SSR markers, 21 CBDP markers, 58 ISJ markers, and 19 SCoT markers (521 polymorphic alleles) distributed on 21 wheat chromosomes. This map covered 3167.9 cM of the wheat genome and had an average marker spacing of 6.1, 6, and 6.2 cM for the A, B, and D genomes, respectively. Thirteen of the fourteen QTLs discovered in 2019 and four of the nine QTLs discovered in 2020 had an explanatory coefficient greater than 15% and were considered major QTLs. In 2019, pleiotropic QTLs were found at position 1.79 cM on chromosome 3A and between two markers Xwmc11-3A and BARC1177. In 2020, two QTLs, qABS/ RC 1B and qTRo/ RC 1B were located at position 36.80 cM 1B and between two markers Xgpw4331-1B and Xgpw5162-1B, and two QTLs, qETo/ RC-5D and qREo / RC-5D were located at position 63.25 cM chromosome 5D and correspond to the position of marker cfd266. Pleiotropic QTLs as well as major QTLs can be used in marker-assisted selection for chlorophyll fluorescence traits in wheat breeding projects.

Assessing the Effect of a Major Quantitative Locus for Phosphorus Uptake (Pup1) in Rice (O. sativa L.) Grown under a Temperate Region

Water and phosphorus (P) fertilizer are two of the most critical inputs in rice cultivation. Irrigation and chemical fertilizers are becoming limiting factors under climate change and urbanization, which is leading to significant losses in yield. The Pup1 quantitative trait locus (QTL) confers tolerance to P starvation through enhanced early-stage root vigor and P uptake in indica rice grown in the tropics. Whether the QTL works in temperate rice genetic backgrounds grown in temperate regions remains to be elucidated. To address this question, we introgressed the Pup1 QTL into three temperate rice varieties—MS11, TR22183, and Dasanbyeo—using marker-assisted backcrossing and high-density genotyping. The selected lines all harbored the full Pup1 QTL with recurrent parent genome recovery rates ranging from 66.5% to 99.8%. Under the rainfed and P non-supplied conditions, Pup1 introgression lines did not show clear advantages over the recurrent parents in terms of vegetative growth and grain yield per plant, but exhibited enhanced yield responses to P application, except in Dasanbyeo, which a temperate rice that is genetically similar to indica. Our results suggest that Pup1 confers enhanced P uptake in temperate rice and that the efficacy of Pup1 might depend on the subspecific genomic background of the rice, whether it is japonica or indica.

Genetic and phenotypic analyses reveal major quantitative loci associated to fruit size and shape traits in a non-flat peach collection (P. persica L. Batsch)

Fruit size and shape are critical agronomical and pomological attributes and prime targets in peach breeding programs. Apart from the flat peach type, a Mendelian trait well-characterized at the genetic level, ample diversity of fruit size and shapes is present across peach germplasms. Nevertheless, knowledge of the underlying genomic loci remains limited. In this work, fruit size and shape were assessed in a collection of non-flat peach accessions and selections, under controlled fruit load conditions. The architecture of these traits was then dissected by combining association and linkage mapping, revealing a major locus on the proximal end of chromosome 6 (qSHL/Fs6.1) explaining a large proportion of phenotypic variability for longitudinal shape and also affecting fruit size. A second major locus for fruit longitudinal shape (qSHL5.1), probably also affecting fruit size, was found co-localizing at locus G, suggesting pleiotropic effects of peach/nectarine traits. An additional QTL for fruit longitudinal shape (qSHL6.2) was identified in the distal end of chromosome 6 in a cross with an ornamental double-flower peach and co-localized with the Di2 locus, controlling flower morphology. Besides assisting breeding activities, knowledge of loci controlling fruit size and shape paves the way for more in-depth studies aimed at the identification of underlying genetic variant(s).

Mapping quantitative trait loci for disease resistance to false smut of rice

False smut of rice, an important emerging disease caused by Ustilaginoidea virens, greatly reduces grain yield and deteriorates grain quality in many rice-growing regions worldwide. Identification of quantitative trait loci (QTL) conferring false smut resistance will facilitate incorporation of false smut resistance into elite cultivars. In this study, a set of recombinant inbred lines (RILs) derived from a cross of a resistant rice landrace MR183–2 and a high susceptible line 08R2394 were evaluated to map resistance QTLs for false smut. A total of 179 simple sequence repeat (SSR) polymorphic markers were identified for constructing genetic linkage maps. Using a composite interval mapping method, five false smut resistance QTLs were detected on chromosomes 2, 4, 8 and 11 in the RIL population. Among these QTLs, qFsr8–1 within a small region on chromosome 8 represents a major quantitative locus explaining the greatest phenotypic variance. Gene annotation in this major QTL region provides a theoretical basis for cloning of resistance QTLs. The SSR markers genetically linked to qFsr8–1 are valuable for marker-assisted breeding for false smut resistance in rice. In addition, nine QTLs for heading date were detected in this population. Correlation analysis of disease resistance score and heading date indicates that false smut resistance negatively correlates with the growth period length in rice.

GSNOR provides plant tolerance to iron toxicity via preventing iron-dependent nitrosative and oxidative cytotoxicity

Iron (Fe) is essential for life, but in excess can cause oxidative cytotoxicity through the generation of Fe-catalyzed reactive oxygen species. It is yet unknown which genes and mechanisms can provide Fe-toxicity tolerance. Here, we identify S-nitrosoglutathione-reductase (GSNOR) variants underlying a major quantitative locus for root tolerance to Fe-toxicity in Arabidopsis using genome-wide association studies and allelic complementation. These variants act largely through transcript level regulation. We further show that the elevated nitric oxide is essential for Fe-dependent redox toxicity. GSNOR maintains root meristem activity and prevents cell death via inhibiting Fe-dependent nitrosative and oxidative cytotoxicity. GSNOR is also required for root tolerance to Fe-toxicity throughout higher plants such as legumes and monocots, which exposes an opportunity to address crop production under high-Fe conditions using natural GSNOR variants. Overall, this study shows that genetic or chemical modulation of the nitric oxide pathway can broadly modify Fe-toxicity tolerance.

Correction for Gao et al., Days to heading 7 , a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice

Correction for Gao et al., <i>Days to heading 7</i> , a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice

Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice.

Success of modern agriculture relies heavily on breeding of crops with maximal regional adaptability and yield potentials. A major limiting factor for crop cultivation is their flowering time, which is strongly regulated by day length (photoperiod) and temperature. Here we report identification and characterization of Days to heading 7 (DTH7), a major genetic locus underlying photoperiod sensitivity and grain yield in rice. Map-based cloning reveals that DTH7 encodes a pseudo-response regulator protein and its expression is regulated by photoperiod. We show that in long days DTH7 acts downstream of the photoreceptor phytochrome B to repress the expression of Ehd1, an up-regulator of the "florigen" genes (Hd3a and RFT1), leading to delayed flowering. Further, we find that haplotype combinations of DTH7 with Grain number, plant height, and heading date 7 (Ghd7) and DTH8 correlate well with the heading date and grain yield of rice under different photoperiod conditions. Our data provide not only a macroscopic view of the genetic control of photoperiod sensitivity in rice but also a foundation for breeding of rice cultivars better adapted to the target environments using rational design.

The A and B loci of Nicotiana tabacum have non-equivalent effects on the mRNA levels of four alkaloid biosynthetic genes

The A and B loci of Nicotiana tabacum are the two major quantitative loci affecting nicotine levels. The A and B loci are thought to be regulatory genes because mutant alleles result in decreased nicotine accumulation and decreased enzyme levels of three nicotine biosynthetic activities. In this report, a combination of RNA gel blot and quantitative real time PCR analysis were performed to determine whether the steady state mRNA accumulation levels of four known multigene families involved in nicotine biosynthesis were also effected by the mutant a and b alleles. The absolute mRNA accumulation levels and relative fold-induction of each multigene family differed among the four multigene families. The homozygous mutant a genotype alone resulted in decreased mRNA accumulation of all four genes, whereas the single homozygous b genotype did not. However, the homozygous double mutant ( aabb) showed lower mRNA accumulation levels than either the single homozygous mutant genotype alone, indicating that the mutant a and b gene products were acting synergistically to further decrease mRNA levels. These results demonstrate that the A and B loci are non-equivalent regulatory loci that decrease the steady state mRNA levels of at least four alkaloid biosynthetic genes.